Merge pull request 'bulkTaggingPathMapExtention' (#381) from bulkTaggingPathMapExtention into beta

Reviewed-on: #381

dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/bipfinder/SparkAtomicActionScoreJob.java

@@ -95,7 +95,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
 
 		return projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> {
 			Project project = new Project();
-			project.setId(bipProjectScores.getProjectId());
+			//project.setId(bipProjectScores.getProjectId());
 			project.setMeasures(bipProjectScores.toMeasures());
 			return project;
 		}, Encoders.bean(Project.class))

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Action.java

@@ -0,0 +1,39 @@
+
+package eu.dnetlib.dhp.bulktag.actions;
+
+import java.io.Serializable;
+import java.util.List;
+
+/**
+ * @author miriam.baglioni
+ * @Date 22/01/24
+ */
+public class Action implements Serializable {
+	private String clazz;
+	private String method;
+	private List<Parameters> params;
+
+	public String getClazz() {
+		return clazz;
+	}
+
+	public void setClazz(String clazz) {
+		this.clazz = clazz;
+	}
+
+	public String getMethod() {
+		return method;
+	}
+
+	public void setMethod(String method) {
+		this.method = method;
+	}
+
+	public List<Parameters> getParams() {
+		return params;
+	}
+
+	public void setParams(List<Parameters> params) {
+		this.params = params;
+	}
+}

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/ExecSubstringAction.java

@@ -0,0 +1,45 @@
+
+package eu.dnetlib.dhp.bulktag.actions;
+
+import java.io.Serializable;
+
+/**
+ * @author miriam.baglioni
+ * @Date 19/01/24
+ */
+public class ExecSubstringAction implements Serializable {
+
+	private String value;
+	private String from;
+	private String to;
+
+	public String getValue() {
+		return value;
+	}
+
+	public void setValue(String value) {
+		this.value = value;
+	}
+
+	public String getFrom() {
+		return from;
+	}
+
+	public void setFrom(String from) {
+		this.from = from;
+	}
+
+	public String getTo() {
+		return to;
+	}
+
+	public void setTo(String to) {
+		this.to = to;
+	}
+
+	public String execSubstring() {
+
+		return this.value.substring(Integer.valueOf(this.from), Integer.valueOf(this.to));
+
+	}
+}

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/MapModel.java

@@ -0,0 +1,30 @@
+
+package eu.dnetlib.dhp.bulktag.actions;
+
+import java.io.Serializable;
+
+/**
+ * @author miriam.baglioni
+ * @Date 22/01/24
+ */
+public class MapModel implements Serializable {
+
+	private String path;
+	private Action action;
+
+	public String getPath() {
+		return path;
+	}
+
+	public void setPath(String path) {
+		this.path = path;
+	}
+
+	public Action getAction() {
+		return action;
+	}
+
+	public void setAction(Action action) {
+		this.action = action;
+	}
+}

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/actions/Parameters.java

@@ -0,0 +1,29 @@
+
+package eu.dnetlib.dhp.bulktag.actions;
+
+import java.io.Serializable;
+
+/**
+ * @author miriam.baglioni
+ * @Date 22/01/24
+ */
+public class Parameters implements Serializable {
+	private String paramName;
+	private String paramValue;
+
+	public String getParamName() {
+		return paramName;
+	}
+
+	public void setParamName(String paramName) {
+		this.paramName = paramName;
+	}
+
+	public String getParamValue() {
+		return paramValue;
+	}
+
+	public void setParamValue(String paramValue) {
+		this.paramValue = paramValue;
+	}
+}

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ProtoMap.java

@@ -4,7 +4,9 @@ package eu.dnetlib.dhp.bulktag.community;
 import java.io.Serializable;
 import java.util.HashMap;
 
-public class ProtoMap extends HashMap<String, String> implements Serializable {
+import eu.dnetlib.dhp.bulktag.actions.MapModel;
+
+public class ProtoMap extends HashMap<String, MapModel> implements Serializable {
 
 	public ProtoMap() {
 		super();

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/community/ResultTagger.java

@@ -5,6 +5,8 @@ import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.*;
 import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
 
 import java.io.Serializable;
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
 import java.util.*;
 import java.util.stream.Collectors;
 
@@ -15,7 +17,10 @@ import org.slf4j.LoggerFactory;
 import com.google.gson.Gson;
 import com.jayway.jsonpath.DocumentContext;
 import com.jayway.jsonpath.JsonPath;
+import com.jayway.jsonpath.PathNotFoundException;
 
+import eu.dnetlib.dhp.bulktag.actions.MapModel;
+import eu.dnetlib.dhp.bulktag.actions.Parameters;
 import eu.dnetlib.dhp.bulktag.eosc.EoscIFTag;
 import eu.dnetlib.dhp.schema.oaf.*;
 import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
@@ -35,27 +40,59 @@ public class ResultTagger implements Serializable {
 		return (tmp != clist.size());
 	}
 
-	private Map<String, List<String>> getParamMap(final Result result, Map<String, String> params) {
+	private Map<String, List<String>> getParamMap(final Result result, Map<String, MapModel> params)
+		throws NoSuchMethodException, InvocationTargetException {
 		Map<String, List<String>> param = new HashMap<>();
 		String json = new Gson().toJson(result, Result.class);
 		DocumentContext jsonContext = JsonPath.parse(json);
+
 		if (params == null) {
 			params = new HashMap<>();
 		}
 		for (String key : params.keySet()) {
+			MapModel mapModel = params.get(key);
+
 			try {
-				param.put(key, jsonContext.read(params.get(key)));
-			} catch (com.jayway.jsonpath.PathNotFoundException e) {
+				String path = mapModel.getPath();
+				Object obj = jsonContext.read(path);
+				List<String> pathValue;
+				if (obj instanceof java.lang.String)
+					pathValue = Arrays.asList((String) obj);
+				else
+					pathValue = (List<String>) obj;
+				if (Optional.ofNullable(mapModel.getAction()).isPresent()) {
+					Class<?> c = Class.forName(mapModel.getAction().getClazz());
+					Object class_instance = c.newInstance();
+					Method setField = c.getMethod("setValue", String.class);
+					setField.invoke(class_instance, pathValue.get(0));
+					for (Parameters p : mapModel.getAction().getParams()) {
+						setField = c.getMethod("set" + p.getParamName(), String.class);
+						setField.invoke(class_instance, p.getParamValue());
+					}
+
+					param
+						.put(
+							key, Arrays
+								.asList((String) c.getMethod(mapModel.getAction().getMethod()).invoke(class_instance)));
+
+				}
+
+				else {
+					param.put(key, pathValue);
+				}
+
+			} catch (PathNotFoundException | ClassNotFoundException | InstantiationException
+				| IllegalAccessException e) {
 				param.put(key, new ArrayList<>());
 			}
 		}
 		return param;
+
 	}
 
 	public <R extends Result> R enrichContextCriteria(
-		final R result, final CommunityConfiguration conf, final Map<String, String> criteria) {
-
-		final Map<String, List<String>> param = getParamMap(result, criteria);
+		final R result, final CommunityConfiguration conf, final Map<String, MapModel> criteria)
+		throws InvocationTargetException, NoSuchMethodException {
 
 		// Verify if the entity is deletedbyinference. In case verify if to clean the context list
 		// from all the zenodo communities
@@ -64,6 +101,8 @@ public class ResultTagger implements Serializable {
 			return result;
 		}
 
+		final Map<String, List<String>> param = getParamMap(result, criteria);
+
 		// Execute the EOSCTag for the services
 		switch (result.getResulttype().getClassid()) {
 			case PUBLICATION_RESULTTYPE_CLASSID:

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/GreatThanVerb.java

@@ -0,0 +1,34 @@
+
+package eu.dnetlib.dhp.bulktag.criteria;
+
+import java.io.Serializable;
+
+/**
+ * @author miriam.baglioni
+ * @Date 11/11/22
+ */
+@VerbClass("greater_than")
+public class GreatThanVerb implements Selection, Serializable {
+
+	private String param;
+
+	public GreatThanVerb() {
+	}
+
+	public GreatThanVerb(final String param) {
+		this.param = param;
+	}
+
+	@Override
+	public boolean apply(String value) {
+		return value.compareTo(param) > 0;
+	}
+
+	public String getParam() {
+		return param;
+	}
+
+	public void setParam(String param) {
+		this.param = param;
+	}
+}

dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/criteria/LessThanVerb.java

@@ -0,0 +1,34 @@
+
+package eu.dnetlib.dhp.bulktag.criteria;
+
+import java.io.Serializable;
+
+/**
+ * @author miriam.baglioni
+ * @Date 11/11/22
+ */
+@VerbClass("lesser_than")
+public class LessThanVerb implements Selection, Serializable {
+
+	private String param;
+
+	public LessThanVerb() {
+	}
+
+	public LessThanVerb(final String param) {
+		this.param = param;
+	}
+
+	@Override
+	public boolean apply(String value) {
+		return value.compareTo(param) < 0;
+	}
+
+	public String getParam() {
+		return param;
+	}
+
+	public void setParam(String param) {
+		this.param = param;
+	}
+}

dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/BulkTagJobTest.java

@@ -13,6 +13,7 @@ import org.apache.commons.io.IOUtils;
 import org.apache.spark.SparkConf;
 import org.apache.spark.api.java.JavaRDD;
 import org.apache.spark.api.java.JavaSparkContext;
+import org.apache.spark.api.java.function.FilterFunction;
 import org.apache.spark.sql.Encoders;
 import org.apache.spark.sql.Row;
 import org.apache.spark.sql.SparkSession;
@@ -31,18 +32,26 @@ public class BulkTagJobTest {
 
 	private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
 
-	public static final String pathMap = "{ \"author\" : \"$['author'][*]['fullname']\","
-		+ "  \"title\" : \"$['title'][*]['value']\","
-		+ "  \"orcid\" : \"$['author'][*]['pid'][*][?(@['key']=='ORCID')]['value']\","
-		+ "  \"contributor\" : \"$['contributor'][*]['value']\","
-		+ "  \"description\" : \"$['description'][*]['value']\", "
-		+ " \"subject\" :\"$['subject'][*]['value']\" , " +
-		"\"fos\" : \"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"," +
-		"\"sdg\" : \"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"," +
-		"\"hostedby\" : \"$['instance'][*]['hostedby']['key']\" , " +
-		"\"collectedfrom\" : \"$['instance'][*]['collectedfrom']['key']\"," +
-		"\"publisher\":\"$['publisher'].value\"," +
-		"\"publicationyear\":\"$['dateofacceptance'].value\"} ";
+	public static final String pathMap = "{\"author\":{\"path\":\"$['author'][*]['fullname']\"}," +
+		" \"title\":{\"path\":\"$['title'][*]['value']\"}, " +
+		" \"orcid\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid')]['value']\"} , " +
+		" \"orcid_pending\":{\"path\":\"$['author'][*]['pid'][*][?(@['qualifier']['classid']=='orcid_pending')]['value']\"} ,"
+		+
+		"\"contributor\" : {\"path\":\"$['contributor'][*]['value']\"}," +
+		" \"description\" : {\"path\":\"$['description'][*]['value']\"}," +
+		" \"subject\" :{\"path\":\"$['subject'][*]['value']\"}, " +
+		" \"fos\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='FOS')].value\"} , " +
+		"\"sdg\" : {\"path\":\"$['subject'][?(@['qualifier']['classid']=='SDG')].value\"}," +
+		"\"journal\":{\"path\":\"$['journal'].name\"}," +
+		"\"hostedby\":{\"path\":\"$['instance'][*]['hostedby']['key']\"}," +
+		"\"collectedfrom\":{\"path\":\"$['instance'][*]['collectedfrom']['key']\"}," +
+		"\"publisher\":{\"path\":\"$['publisher'].value\"}," +
+		"\"publicationyear\":{\"path\":\"$['dateofacceptance'].value\", " +
+		" \"action\":{\"clazz\":\"eu.dnetlib.dhp.bulktag.actions.ExecSubstringAction\"," +
+		"\"method\":\"execSubstring\"," +
+		"\"params\":[" +
+		"{\"paramName\":\"From\",  \"paramValue\":0}, " +
+		"{\"paramName\":\"To\",\"paramValue\":4}]}}}";
 
 	private static SparkSession spark;
 
@@ -1600,4 +1609,94 @@ public class BulkTagJobTest {
 		Assertions.assertEquals(0, spark.sql(query).count());
 	}
 
+	@Test
+	void pubdateTest() throws Exception {
+
+		final String pathMap = BulkTagJobTest.pathMap;
+		SparkBulkTagJob
+			.main(
+				new String[] {
+					"-isSparkSessionManaged", Boolean.FALSE.toString(),
+					"-sourcePath",
+					getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/publicationyear/").getPath(),
+					"-taggingConf",
+					IOUtils
+						.toString(
+							BulkTagJobTest.class
+								.getResourceAsStream(
+									"/eu/dnetlib/dhp/bulktag/communityconfiguration/tagging_conf_publicationdate.xml")),
+					"-outputPath", workingDir.toString() + "/",
+					"-pathMap", pathMap
+				});
+
+		final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
+
+		JavaRDD<Dataset> tmp = sc
+			.textFile(workingDir.toString() + "/dataset")
+			.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
+
+		Assertions.assertEquals(10, tmp.count());
+		org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
+			.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
+
+		verificationDataset.createOrReplaceTempView("dataset");
+
+		String query = "select id, MyT.id community, MyD.provenanceaction.classid "
+			+ "from dataset "
+			+ "lateral view explode(context) c as MyT "
+			+ "lateral view explode(MyT.datainfo) d as MyD "
+			+ "where MyD.inferenceprovenance = 'bulktagging'";
+
+		org.apache.spark.sql.Dataset<Row> queryResult = spark.sql(query);
+		queryResult.show(false);
+		Assertions.assertEquals(5, queryResult.count());
+
+		Assertions
+			.assertEquals(
+				1,
+				queryResult
+					.filter(
+						(FilterFunction<Row>) r -> r
+							.getAs("id")
+							.equals("50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529"))
+					.count());
+		Assertions
+			.assertEquals(
+				1,
+				queryResult
+					.filter(
+						(FilterFunction<Row>) r -> r
+							.getAs("id")
+							.equals("50|od______3989::2f4f3c820c450bd08dac08d07cc82dcf"))
+					.count());
+		Assertions
+			.assertEquals(
+				1,
+				queryResult
+					.filter(
+						(FilterFunction<Row>) r -> r
+							.getAs("id")
+							.equals("50|od______3989::7fcbe3a03280663cddebfd3cb9203177"))
+					.count());
+		Assertions
+			.assertEquals(
+				1,
+				queryResult
+					.filter(
+						(FilterFunction<Row>) r -> r
+							.getAs("id")
+							.equals("50|od______3989::d791339867bec6d3eb2104deeb4e4961"))
+					.count());
+		Assertions
+			.assertEquals(
+				1,
+				queryResult
+					.filter(
+						(FilterFunction<Row>) r -> r
+							.getAs("id")
+							.equals("50|od______3989::d90d3a1f64ad264b5ebed8a35b280343"))
+					.count());
+
+	}
+
 }